adjusted some of the values for tissue with no signal

oliverchampion · oliverchampion · commit d76735f4a675 · 2024-08-14T10:38:02.000+02:00
diff --git a/phantoms/MR_XCAT_qMRI/sim_ivim_sig.py b/phantoms/MR_XCAT_qMRI/sim_ivim_sig.py
@@ -99,7 +99,7 @@ def contrast_curve_calc():
     D[17] = 1.67e-3  # 17 esophagus : Huang et al. doi: 10.1259/bjr.20170421
     D[18] = 1.67e-3  # 18 esophagus cont : Huang et al. doi: 10.1259/bjr.20170421
     D[20] = 1.5e-3  # 20 stomach wall: Li et al. doi: 10.3389/fonc.2022.821586
-    D[21] = 2.0e-3  # 21 stomach content
+    D[21] = 3.0e-3  # 21 stomach content
     D[22] = 1.3e-3  # 22 Pancreas (from literature)
     D[23] = 2.12e-3  # 23 right kydney cortex : van Baalen et al. Doi: jmri.25519
     D[24] = 2.09e-3  # 23 right kydney medulla : van Baalen et al. Doi: jmri.25519
@@ -165,7 +165,7 @@ def contrast_curve_calc():
     Ds[17] = 0.03  # 17 esophagus : Huang et al. doi: 10.1259/bjr.20170421
     Ds[18] = 0.03  # 18 esophagus cont : Huang et al. doi: 10.1259/bjr.20170421
     Ds[20] = 0.012  # 20 stomach wall: Li et al. doi: 10.3389/fonc.2022.821586
-    Ds[21] = 0.1  # 20 stomach content
+    Ds[21] = 0.0  # 20 stomach content
     Ds[22] = 0.01  # 22 Pancreas (from literature)
     Ds[23] = 0.02  # 23 right kydney cortex : van Baalen et al. Doi: jmri.25519
     Ds[24] = 0.019  # 23 right kydney medulla : van Baalen et al. Doi: jmri.25519
@@ -297,7 +297,7 @@ def XCAT_to_MR_DCE(XCAT, TR, TE, bvalue, D, f, Ds, b0=3, ivim_cont = True):
     Tissue[19] = [1045.5, 37.3, 1201, 44]
     Tissue[20] = [981.5, 36, 1232.9, 37.20]
     #Tissue[20] = [981.5, 36, 1232.9, 37.20]
-    Tissue[21] = [0, 0, 0, 0]
+    Tissue[21] = [2500, 1250, 4000, 2000]
     Tissue[22] = [584, 46, 725, 43]
     Tissue[23] = [828, 71, 1168, 66]
     Tissue[24] = [1412, 85, 1545, 81]
diff --git a/tests/IVIMmodels/unit_tests/generic.json b/tests/IVIMmodels/unit_tests/generic.json
@@ -287,28 +287,28 @@
     },
     "Stomach Contents": {
         "noise": 0.0005,
-        "D": 0.002000000000000001,
+        "D": 0.0030000000000000005,
         "f": 0.0,
-        "Dp": 0.10000000000000002,
+        "Dp": 0.0,
         "data": [
-            5.80074394810416e-05,
-            5.107581409413805e-05,
-            -0.00012425433616179758,
-            -0.0003012924365816795,
-            0.00012758643047470927,
-            0.0004170165250105098,
-            8.461158236131148e-05,
-            -0.00016202394652097316,
-            -0.000958161107821496,
-            0.000452036540223895,
-            -0.0006338373896442981,
-            -6.407697371328715e-05,
-            6.664092464539553e-05,
-            0.0005538785306771071,
-            -1.2423671933829899e-05,
-            0.0004053531904869084,
-            7.083433682752305e-05,
-            0.0008320566959464623
+            0.5126018871088376,
+            0.5110596279871825,
+            0.5093535694210771,
+            0.5046118029961769,
+            0.4975235052032258,
+            0.4831126643032834,
+            0.4685144470320901,
+            0.44098858155273923,
+            0.4083164396340143,
+            0.3801538814981812,
+            0.32617856922898014,
+            0.24204450859420612,
+            0.17942509249683888,
+            0.15492912843811152,
+            0.09842158158269289,
+            0.06316964601772247,
+            0.04009111436010544,
+            0.02635011387457495
         ]
     },
     "pancreas": {
diff --git a/tests/IVIMmodels/unit_tests/generic_four.json b/tests/IVIMmodels/unit_tests/generic_four.json
@@ -287,28 +287,28 @@
     },
     "Stomach Contents": {
         "noise": 0.0005,
-        "D": 0.002000000000000001,
+        "D": 0.0030000000000000005,
         "f": 0.0,
-        "Dp": 0.10000000000000002,
+        "Dp": 0.0,
         "data": [
-            5.80074394810416e-05,
-            5.107581409413805e-05,
-            -0.00012425433616179758,
-            -0.0003012924365816795,
-            0.00012758643047470927,
-            0.0004170165250105098,
-            8.461158236131148e-05,
-            -0.00016202394652097316,
-            -0.000958161107821496,
-            0.000452036540223895,
-            -0.0006338373896442981,
-            -6.407697371328715e-05,
-            6.664092464539553e-05,
-            0.0005538785306771071,
-            -1.2423671933829899e-05,
-            0.0004053531904869084,
-            7.083433682752305e-05,
-            0.0008320566959464623
+            0.5126018871088376,
+            0.5110596279871825,
+            0.5093535694210771,
+            0.5046118029961769,
+            0.4975235052032258,
+            0.4831126643032834,
+            0.4685144470320901,
+            0.44098858155273923,
+            0.4083164396340143,
+            0.3801538814981812,
+            0.32617856922898014,
+            0.24204450859420612,
+            0.20845143168394226,
+            0.15492912843811152,
+            0.11435157428178726,
+            0.0851282866646102,
+            0.06283512716406309,
+            0.047328988430565426
         ]
     },
     "pancreas": {
diff --git a/tests/IVIMmodels/unit_tests/generic_one.json b/tests/IVIMmodels/unit_tests/generic_one.json
@@ -309,30 +309,30 @@
     },
     "Stomach Contents": {
         "noise": 0.0005,
-        "D": 0.002000000000000001,
+        "D": 0.0030000000000000005,
         "f": 0.0,
-        "Dp": 0.10000000000000002,
+        "Dp": 0.0,
         "data": [
-            -0.0006891569843084475,
-            -0.000350349205760221,
-            -0.000917113669609909,
-            4.602241579321293e-08,
-            -0.00018302139591143602,
-            0.00018186374664528606,
-            -0.0004530159152872634,
-            2.8535519125183674e-05,
-            -0.00045237992205407436,
-            0.0001590664107331867,
-            -0.0002977007140224263,
-            0.0001680245153855177,
-            -0.00021378084344275637,
-            -2.973881510708059e-05,
-            -0.0005213401147112412,
-            -0.00018130926334482638,
-            -0.00029702560689974104,
-            0.0001829254096871082,
-            -6.193284334855272e-05,
-            4.118162939074253e-05
+            0.5118547226850481,
+            0.5106582029673281,
+            0.508560710087629,
+            0.5049131414551744,
+            0.49721289737683966,
+            0.4828775115249182,
+            0.46797681953444153,
+            0.4411791410183854,
+            0.40882222081978176,
+            0.3798609113686905,
+            0.326514705904602,
+            0.24227661008330495,
+            0.17914467072875073,
+            0.1543455110923273,
+            0.09791266513991548,
+            0.06258298356389073,
+            0.03972325441637818,
+            0.025700982588315595,
+            0.018842308870977337,
+            0.014045788339534756
         ]
     },
     "pancreas": {
diff --git a/tests/IVIMmodels/unit_tests/generic_three.json b/tests/IVIMmodels/unit_tests/generic_three.json
@@ -276,27 +276,27 @@
     },
     "Stomach Contents": {
         "noise": 0.0005,
-        "D": 0.002000000000000001,
+        "D": 0.0030000000000000005,
         "f": 0.0,
-        "Dp": 0.10000000000000002,
+        "Dp": 0.0,
         "data": [
-            -0.00015283463313758177,
-            0.0001016610871739754,
-            0.0007074038187109081,
-            0.00036841293881897637,
-            0.00021476864205758202,
-            0.0003864380804761366,
-            -0.0009806012679601853,
-            0.0007615651897909676,
-            7.007298111510775e-05,
-            -0.0007165444873753203,
-            0.0004936886427893894,
-            0.0018016206647201063,
-            -0.0004921881101895262,
-            0.00032495269107461994,
-            0.00036673577745912576,
-            7.404966351412328e-05,
-            6.03246126200487e-05
+            0.512391045036219,
+            0.5111102132602624,
+            0.5101852275759499,
+            0.5052815083715776,
+            0.4976106874148087,
+            0.483082085858749,
+            0.4674492341817686,
+            0.4419121706890512,
+            0.4093446737229509,
+            0.37898530047058193,
+            0.3273060952614138,
+            0.24391020623263954,
+            0.17886626346200396,
+            0.13319696164901507,
+            0.09880074103208585,
+            0.0677266861434733,
+            0.04655725634723901
         ]
     },
     "pancreas": {
diff --git a/tests/IVIMmodels/unit_tests/generic_two.json b/tests/IVIMmodels/unit_tests/generic_two.json
@@ -309,30 +309,30 @@
     },
     "Stomach Contents": {
         "noise": 0.0005,
-        "D": 0.002000000000000001,
+        "D": 0.0030000000000000005,
         "f": 0.0,
-        "Dp": 0.10000000000000002,
+        "Dp": 0.0,
         "data": [
-            -0.0006891569843084475,
-            -0.000350349205760221,
-            -0.000917113669609909,
-            4.602241579321293e-08,
-            -0.00018302139591143602,
-            0.00018186374664528606,
-            -0.0004530159152872634,
-            2.8535519125183674e-05,
-            -0.00045237992205407436,
-            0.0001590664107331867,
-            -0.0002977007140224263,
-            0.0001680245153855177,
-            -0.00021378084344275637,
-            -2.973881510708059e-05,
-            -0.0005213401147112412,
-            -0.00018130926334482638,
-            -0.00029702560689974104,
-            0.0001829254096871082,
-            -6.193284334855272e-05,
-            4.118162939074253e-05
+            0.5118547226850481,
+            0.5106582029673281,
+            0.508560710087629,
+            0.5049131414551744,
+            0.49721289737683966,
+            0.4828775115249182,
+            0.46797681953444153,
+            0.4411791410183854,
+            0.40882222081978176,
+            0.3798609113686905,
+            0.326514705904602,
+            0.24227661008330495,
+            0.17914467072875073,
+            0.1543455110923273,
+            0.11384265783900985,
+            0.06258298356389073,
+            0.04619990612771922,
+            0.025700982588315595,
+            0.018842308870977337,
+            0.014045788339534756
         ]
     },
     "pancreas": {
diff --git a/tests/IVIMmodels/unit_tests/test_ivim_fit.py b/tests/IVIMmodels/unit_tests/test_ivim_fit.py
@@ -169,6 +169,8 @@ def test_ivim_fit_saved(name, bvals, data, algorithm, xfail, kwargs, tolerances,
     tolerances = tolerances_helper(tolerances, ratio, data["noise"])
     [f_fit, Dp_fit, D_fit] = fit.osipi_fit(signal, bvals)
     npt.assert_allclose(data['f'], f_fit, rtol=tolerances["rtol"]["f"], atol=tolerances["atol"]["f"])
-    npt.assert_allclose(data['D'], D_fit, rtol=tolerances["rtol"]["D"], atol=tolerances["atol"]["D"])
-    npt.assert_allclose(data['Dp'], Dp_fit, rtol=tolerances["rtol"]["Dp"], atol=tolerances["atol"]["Dp"])
+    if data['f']<0.80: # we need some signal for D to be detected
+        npt.assert_allclose(data['D'], D_fit, rtol=tolerances["rtol"]["D"], atol=tolerances["atol"]["D"])
+    if data['f']>0.03: #we need some f for D* to be interpretable
+        npt.assert_allclose(data['Dp'], Dp_fit, rtol=tolerances["rtol"]["Dp"], atol=tolerances["atol"]["Dp"])
 
